The ability to determine the myelin water fraction (MWF) in vivo is essential to assessments of neurodevelopmental myelination and myelin damage in neurodegenerative diseases. The analysis of multi-exponential T2 decay data relies on the non-negative-least-squares (NNLS) fitting, which may be sensitive to the chosen fitting parameters. We performed simulations to explore the outcomes of NNLS under different parameter selection. The lowest allowed T2 was found to have the largest effect on correctly estimating the T2 of different water pools as well as the MWF. Lower refocusing FAs led to further underestimation of the MWF.